Kovalyov was one of a group of activists who set up the Action Group for the Defense of Human Rights in the USSR in 1969, the first such independent body in the Soviet Union.[1][2]:343 While the 14 members of the group and 38 supporters signed their Appeal to the UN Human Rights Commission a number of them were also becoming involved in the samizdat (self-published) human rights bulletin, the Chronicle of Current Events (1968–1983).[3] The members of the Action Group came under pressure from the authorities [4] and ceased their activities.

After the arrest of Pyotr Yakir the Chronicle did not appear for over a year. On 7 May 1974 Kovalyov, Tatyana Velikanova and Tatyana Khodorovich gave a press conference for foreign journalists, declaring their determination to renew publication of the bulletin and distributing three postponed issues.[7] As a consequence Sergei Kovalyov was arrested in Moscow later that year, on December 27, 1974,[8] tried in Vilnius, and charged with "anti-Soviet agitation and propaganda" (Article 70 of the RSFSRPenal Code).[9] He served seven years in penitentiary facilities for political prisoners — the labor camps in the Perm Region and Chistopol Prison — followed by three years of internal exile in Kolyma in the Soviet Far East. Upon his return, he settled in Kalinin (now Tver). He moved back to Moscow in 1987.

During perestroika initiated by Mikhail Gorbachev, Kovalyov was allowed to return to Moscow (in 1986). In that period, he continued his activism and participated in the founding of several key humanitarian organizations and initiatives:

The human rights society Memorial, dedicated to the memory and rehabilitation of victims of political repression in the Soviet Union. Kovalyov has served as its co-chairman since 1990.

From 1990 to 1993, he was an elected People's Deputy of the Russian Federation, and a member of the Presidium of the Supreme Council of the Russian Federation. He served as the chairman of the President's Human Rights Commission and Human Rights Commissioner for the Russian parliament, the State Duma.

From 1993 until 2003, Kovalyov was a member of the Russian State Duma. From 1996 to 2003 he was also a member of the Russian delegation to the Parliamentary Assembly of the Council of Europe and a member of the Assembly's Committee on Legal Affairs and Human Rights.

In 1993, he co-founded the movement and later, the political party Choice of Russia (Выбор России), later renamed Democratic Choice of Russia (Демократический выбор России).

Since 1994, Kovalyov, then Yeltsin's human rights adviser, has been publicly opposed to Russia's military involvement in Chechnya, cooperating with the rebels and urging Russian soldiers to give up. From Grozny, he witnessed and reported the realities of the First Chechen War. His daily reports via telephone and on TV galvanized Russian public opinion against the war. For his activism, he was removed from his post in the Duma in 1995.[10] In 1994, he was awarded the Homo Homini Award for human rights activism by the Czech group People in Need.[11]

Sergei Kovalyov was accused by Russian General Troshev, that during the Battle of Grozny, Kovalyov offered Russian soldiers to surrender. He promised that their life, health and honor would be preserved. But most of those who gave up were killed.[12] However, Mr.Troshev is the only source of this information. Russian nationalist Alexander Prokhanov in his Zavtra newspaper also accused Kovalyov in mistreatment of soldier Yevgeny Rodionov mother, Lyubov Vasilievna. According to Prokhanov, she asked Kovalyov's help in finding her kidnapped and later killed son in 1996, but he roared in response: "Why did you come to me? You raised the murderer".[13]

Kovalyov is a recipient of numerous awards and honorary titles. In 2004, he was awarded the Victor Gollancz Prize by the Society for Threatened Peoples, for documenting Russian crimes in Chechnya. In 2011, he was honored with the Lithuanian Freedom Award for his adherence to democratic values and ideals of freedom.[21][22]